LncRNAs: Bridging environmental sensing and gene expression

Figures & data

Figure 1. A model for regulation of the GAL cluster by GAL lncRNA R-loops and Dbp2. (A) Glucose Repression When glucose is available, Dbp2 is localized in the nucleus⁷⁴ and prevents the accumulation of R-loops at the GAL gene cluster⁵³ via the assembly of Dbp2-dependent lncRNA-protein complexes.⁵⁶ This allows the successful docking of the Cyc8/Tup1 co-repressor complex and subsequent repression. (B) Carbon Source Switch During a switch from glucose to galactose, Dbp2 is actively relocalized to the cytoplasm via export through the nuclear pore complex (NPC).⁷⁴ This may alter lncRNP assembly and cause R-loop formation and spreading across the GAL cluster. R-loop formation likely interferes with binding of transcriptional repressors and the Cyc8/Tup1 corepressor complex, causing derepression of the GAL genes. (C) Galactose Induction In the presence of galactose, the Gal4 transcriptional activator is released from the Gal80 inhibitor (not pictured),⁹⁶ enabling recruitment of co-activators and RNA P II.⁹⁷ This results in altered chromatin structure, as evidenced by looping of the GAL10 promoter and terminator,⁵³ which may enhance transcriptional induction. It is currently unknown how the GAL lncRNAs are cleared from chromatin or how Dbp2 is re-imported following long-term growth in galactose.

Table 1. Individually characterized lncRNAs of Saccharomyces cerevisiae. 65% of functionally characterized lncRNAs in S. cerevisiae have gene targets that function in pathways associated with metabolism or nutrient sensing/transport. AS = antisense. Us = upstream.

Functionally characterized lncRNAs in S. cerevisiae.
Name	Function	Target Gene	Target gene function	Metabolism/Nutrition related
MMF1 AS RNA^Citation29	Promotes induction	MMF1	Mitochondrial protein	YES
ASP3 lncRNA^Citation98	Upregulation	ASP3	Asparagine catabolism	YES
PHO84 AS RNA^Citation99-Citation101	Repression	PHO84	Phosphate metabolism	YES
SRG1^Citation28,Citation50,Citation51	Repression	SER3	Serine / glycine biogenesis	YES
PHO5 AS RNA^Citation102	Promotes induction	PHO5	Phosphate metabolism	YES
usURA2.^Citation103	Repression	URA2	Pyrimidine biogenesis	YES
usDCI1.^Citation104	Repression	DCI1	Fatty acid metabolism	YES
GAL10 lncRNA^Citation47,Citation48,Citation105	Repression	GAL genes	Galactose metabolism	YES
GAL10/GAL10s lncRNAs.^Citation52,Citation53	Promotes induction	GAL genes	Galactose metabolism	YES
KCS1 lncRNAs^Citation106	Translational interference	KCS1	Inositol hexa/hepta bisphosphate kinase	YES
SUT719^Citation30,Citation35	Repression	SUR7	Plasma membrane protein	YES
CDC28 AS RNA^Citation29	Promotes induction	CDC28	Cell cycle regulator	NO
RTL.^Citation107	Repression	Ty1	Retrotransposon	NO
ICR1.^Citation108	Repression	FLO11	Cell surface glycoprotein	NO
PWR1.^Citation108	Upregulation	FLO11	Cell surface glycoprotein	NO
IME4 AS RNA^Citation109,Citation110	Repression	IME4	Meiosis regulator	NO
IRT1.^Citation109	Repression	IME1	Meiosis regulator	NO

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